# Maintainer: bipin kumar <bipin@ccmb.res.in>
# Contributor: sukanka <su975853527 at gmail>
pkgname=augustus
_pkgname=Augustus
pkgver=3.5.0
pkgrel=1
pkgdesc="A eukaryotic gene prediction program"
arch=('i686' 'x86_64')
url="http://bioinf.uni-greifswald.de/augustus/"
license=('custom:Artistic-2.0')
depends=('bamtools'  'boost-libs' 'gsl' 'mysql++' 'sqlite' 'python' 'lpsolve' 'perl' 'htslib')
makedepends=('boost' 'suitesparse' 'samtools' )
source=($pkgname-$pkgver.tar.gz::https://github.com/Gaius-Augustus/Augustus/archive/v$pkgver.tar.gz)
sha256sums=('5ed6ce6106303b800c5e91d37a250baff43b20824657b853ae04d11ad8bdd686')

prepare() {
  cd $_pkgname-$pkgver
  sed -i "s|/usr/local/bin|/usr/bin|" Makefile
}

build() {
  cd $_pkgname-$pkgver
  make SAMTOOLS=/usr/include/bam PREFIX="$pkgdir"/usr INSTALLDIR=${pkgdir}/opt/augustus
}

package() {
  cd $_pkgname-$pkgver
  install -d ${pkgdir}/usr/bin
  make DESTDIR="$pkgdir" PREFIX="$pkgdir"/usr INSTALLDIR=${pkgdir}/opt/augustus install

  # fix broken links
  for bin in {augustus,etraining,prepareAlign,fastBlockSearch}
  do
    ln -sf /opt/augustus/bin/${bin} "$pkgdir"/usr/bin/${bin}
  done
  rm "$pkgdir"/usr/bin/{load2db,getSeq}

  install -Dm644 src/LICENSE.TXT "$pkgdir"/usr/share/licenses/augustus/LICENSE
}